Although physical harm may not befall people within flash games are there any boundaries one should be aware of when programming a flash game or any specific rules to abide by?
If I'm interpreting you correctly then all you need to abide by are the rules of the site, and make sure that your game is suitable for a "teen" audience since you need to be 13+ to even have an account on this site.
Specifically I'm curious of the relationship between Armorgames and flash game developers and the ethical relationships between the two.
I don't think there's a relationship between most of them at all. You don't need to have a relationship with them to submit a game, and they probably won't care to have one. All you need to worry about is that if your game is good enough to be on the site (check some of the current games on the site if you want to see the quality of those), make sure it's suitable for the users of this site (no excessive profanity, etc. just stick with the things mentioned in the rules), and that's about it I believe.